Systems and methods for spatial mapping of expression profiling

Abstract

Systems, apparatuses and methods for spatially mapping at least one biological expression of a target biological component contained in a tissue sample to an image of the tissue sample are provided. In some embodiments, the system includes a processor and instructions that, when executed by the processor, cause the system to display, in a first display, a scans pane including at least the image of the tissue sample, the image including at least one demarcation corresponding to a region-of-interest (ROI(s)), where the ROI(s) correspond to a portion of the tissue within the tissue image. The instructions are further configured to cause the system to display, in a second display, a visualization pane including a visualization of the biological expression contained in the ROI(s); and to augment the first display by coding the ROI(s) in the tissue image to show the spatial mapping of the biological expression within the ROI(s).

1 . A digital analyzer for performing data collection and analysis on a tissue sample comprising:
 a multiplexed analysis device;   a scanner;   a reading device; and   a counting device,   wherein the digital analyzer is configured to:
 a) contact at least one protein target in or from at least one cell in a tissue sample with at least one probe comprising a target-binding domain and a signal oligonucleotide; 
 b) provide or apply a force to a location of the tissue sample sufficient to release the signal oligonucleotide; and 
 c) collect and identify the released signal oligonucleotide, to thereby detect the at least one target in or from a specific location of the tissue sample that was provided the force, wherein the specific location includes a Region of Interest (ROI). 
   
     
     
         2 . The digital analyzer of  claim 1 , wherein the digital analyzer is configured to repeat steps (b) and (c) on at least a second specific location of the tissue sample. 
     
     
         3 . The digital analyzer of  claim 2 , wherein the digital analyzer is configured for comparing the abundance of the at least one protein target in or from the first specific location and in or from the at least second specific location. 
     
     
         4 . The digital analyzer of  claim 2 , wherein the digital analyzer is configured for quantifying the abundance of the at least one protein target in or from a first cell type and in or from at least a second cell type. 
     
     
         5 . The digital analyzer of  claim 4 , further wherein the first and second cell types can be independently selected from a normal cell and a diseased and cancerous cell. 
     
     
         6 . The digital analyzer of  claim 1 , wherein the digital analyzer is further configured to detect using a polymerase reaction, a reverse transcriptase reaction, hybridization to an oligonucleotide microarray, mass spectrometry, hybridization to a fluorescent molecular beacon, a sequencing reaction, or a machine-reading of machine-readable identifiers. 
     
     
         7 . The digital analyzer of  claim 1 , wherein the scanner comprises a barcode scanner. 
     
     
         8 . The digital analyzer of  claim 1 , wherein the digital analyzer further comprises a transducer. 
     
     
         9 . The digital analyzer of  claim 8 , wherein the transducer comprises an energy source, an energy emitter, or a light source. 
     
     
         10 . The digital analyzer of  claim 9 , wherein the digital analyzer is configured to illuminate with a laser scanning device. 
     
     
         11 . The digital analyzer of  claim 1 , wherein the digital analyzer is configured to illuminate and image the tissue sample and to subsequently receive user input specifying a selection of one or more ROIs based on the image of the sample, and to irradiate the tissue sample at one or more of the ROIs to thereby cleave the associated oligonucleotides. 
     
     
         12 . The digital analyzer of  claim 11 , wherein the digital analyzer is configured to collect the cleaved oligonucleotides, and to quantitate the collected and cleaved oligonucleotides to determine: one or more biological expressions contained within at least the one or more ROIs, and their corresponding location therein. 
     
     
         13 . The digital analyzer of  claim 1 , wherein the ROI comprises a user-defined region of a tissue, a user-defined cell, or a user-defined subcellular structure within a cell. 
     
     
         14 . The digital analyzer of  claim 1 , wherein target-binding domain includes a protein-binding molecule. 
     
     
         15 . The digital analyzer of  claim 14 , wherein the protein-binding molecule includes an antibody, a peptide, an aptamer, or a peptoid. 
     
     
         16 . The digital analyzer of  claim 1 , wherein the digital analyzer comprises an image capture device. 
     
     
         17 . The digital analyzer of  claim 16 , wherein the image capture device comprises a charged-couple device or a microscope objective lens.